JC virus (JCV) is a small DNA virus of the polyomavirus genus that is the agent of the subacute CNS demyelinating disease, progressive multifocal leukoencephalopathy (PML). The closely related human polyomavirus, BK virus, infects only the kidney, and has been implicated in kidney transplant failure. PML is the cause of death in approximately 5% of AIDS patients in the USA. JCV is excreted in the urine of healthy individuals and infects almost the entire population worldwide. Much of our effort in this project have been directed at characterizing the natural variation in the DNA sequence that occurs in both the regulatory region and the coding region of the viral genome, and determining the significance of these rearrangements and mutations for both the biology of the virus, and the pathogenesis of the CNS disease. As an added benefit, JCV has proved to be a useful marker of human populations as the virus evolved with the human species and remains strongly population associated. The regulatory region of virus excreted from the kidney is quite stable (archetypal) when circulating in the population, but rearranges extensively by unknown mechanisms before it attacks the brain of immunocompromised individuals. These brain adapted variants are each unique in their regulatory regions, and fortunately, appear not to be more readily transmissible from the urine. The concern is that with more PML present in the population, brain-adapted virus that also has a selective advantage in the kidney might begin to circulate in the population, putting infected individuals at higher risk of brain disease. As part of our worldwide survey of JCV, we have studied JCV from the highlands of Papua New Guinea (PNG) and from two ethnic groups on the nearby island of New Britain: the non-Austronesian-speaking Baining and the Austronesian-speaking Tolai. In PNG we identified three new JCV variants in the VP1 gene typing region (PNG-1, PNG-2 and PNG-3). PNG-2 strains were restricted to the Highlanders. The regulatory regions of PNG-2 variants have a unique deletion with a nested duplication reminiscent of the changes seen in brains of PML patients. This is the first complex rearrangement in JCV (deletion with duplication) found to be excreted widely in a human population. A subtype of the PNG-2 group (PNG-2B) has a novel deletion in the agnogene that removes amino acids 57-63 of this 71-aa protein. We suggest that both the regulatory region rearrangement and the agnoprotein deletion give these variants a selective advantage promoting their spread within the Highlands. This hypothesis will be tested in the laboratory. In addition, AIDS is now increasing in PNG, and surveillance for PML there may reveal whether unusual variants such as PNG-2B have increased neurotropism or neurovirulence.